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近段时间看了这个帖子，觉得用相同的方法做十六烷基三甲基溴化铵和水杨酸钠在水中的构象，也是可以的。于是开始动手实施。
使用genmer得到50个初始结构，每个结构都是1个CTAB+1个NaSal，使用orca5.0.2, g16, xtb6.4.1
1.操作描述
前几个步骤调用xtb计算，自我感觉没有错误，到了用Molclus调用Gaussian和ORCA得到水环境下的高精度自由能这一步，就开始有问题了。 (备注：目前只想试试走通这个流程，没有十分关注精度，等参加下一期量化培训后，再仔细来调到自己觉得合适的精度)
2.调用gaussian+orca使用的文件
这是该步骤用的traj.xyz文件
traj.xyz
(146.26 KB, 下载次数 Times of downloads: 1)
以下是template.gjf内容
- #p B3LYP/6-31G* em=GD3BJ opt freq int=fine SCF(novaracc,noincfock) int=acc2e=12
- Template file
- 0 1
- [GEOMETRY]
以下是template_SP.gjf内容
- ! wB97M-V def2-TZVP def2/J RIJCOSX strongSCF noautostart miniprint nopop
- %maxcore 1000
- %pal nprocs 16 end
- %cpcm
- smd true
- SMDsolvent "water"
- end
- * xyz 0 1
- [GEOMETRY]
- *
3.调用gaussian+orca运行中的提示
*** Configuration 1 ***
Current date: 2022-03-07 Time: 15:37:50
Loading geometry 1 from the inputted trajectory file
Generating gau.gjf...
Running Gaussian: "/home/jing/g16/g16" < gau.gjf > gau.out
Fine, optimization normally converged
Note: Unable to locate "Input orientation" field, try to load standard orientation instead
Opt + freq task normally terminated
Thermal correction to Gibbs free energy: 0.636409 a.u.
Gibbs free energy: -4033.159292 a.u.
Fine, there is no imaginary frequency
Now run single point task based on the template_SP.inp in current folder
Running ORCA: "/home/jing/orca502/orca" orcaSP.inp > orcaSP.out
Deleting orcaSP.* orcaSP_*
Single point calculation normally terminated. The sum of the new single point energy and thermal correction to Gibbs free energy is -4035.190978 a.u.
Writing the converged geometry, free energy and so on to isomers.xyz
Wall clock time elapsed for calculating this configuration: 5751 s
*** Configuration 2 ***
Current date: 2022-03-07 Time: 17:13:41
Loading geometry 2 from the inputted trajectory file
Generating gau.gjf...
Running Gaussian: "/home/jing/g16/g16" < gau.gjf > gau.out
Error: segmentation violation
rax 0000000000000000, rbx ffffffffffffffff, rcx ffffffffffffffff
rdx 000000000000f266, rsp 00007ffd3f8a1d78, rbp 00007ffd3f8a22f0
rsi 000000000000000b, rdi 000000000000f266, r8 0000000000000020
r9 0000000000000401, r10 00007ffd3f8a1160, r11 0000000000000206
r12 00007ffd3f8a2338, r13 0000000000000000, r14 0000000000000000
r15 00000000000003e6
/lib64/libpthread.so.0(+0xf630) [0x2b38240ee630]
/lib64/libc.so.6(kill+0x7) [0x2b3824633657]
/home/jing/g16/l502.exe() [0x475c25]
/home/jing/g16/l502.exe() [0x49b42a]
/home/jing/g16/l502.exe() [0x5183db]
/home/jing/g16/l502.exe() [0x4f72af]
/home/jing/g16/l502.exe() [0x41de12]
/home/jing/g16/l502.exe() [0x4129db]
/home/jing/g16/l502.exe() [0x4128e4]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x2b382461f555]
/home/jing/g16/l502.exe() [0x40d029]
Error: Optimization did not normally finish!
The optimization failed due to certain reason, e.g. SCF unconvergence, three atoms are lying in the same line
Generate new gau.gjf with the last unconverged geometry based on template2.gjf
Note: Unable to locate "Input orientation" field, try to load standard orientation instead
Running Gaussian: "/home/jing/g16/g16" < gau.gjf > gau.out
Error: segmentation violation
rax 0000000000000000, rbx ffffffffffffffff, rcx ffffffffffffffff
rdx 000000000000f69e, rsp 00007ffc4c9b1f18, rbp 00007ffc4c9b2490
rsi 000000000000000b, rdi 000000000000f69e, r8 0000000000000020
r9 0000000000000401, r10 00007ffc4c9b1320, r11 0000000000000206
r12 00007ffc4c9b24d8, r13 0000000000000000, r14 0000000000000000
r15 00000000000003e6
/lib64/libpthread.so.0(+0xf630) [0x2b78c841f630]
/lib64/libc.so.6(kill+0x7) [0x2b78c8964657]
/home/jing/g16/l9999.exe() [0x45da85]
/home/jing/g16/l9999.exe() [0x478bea]
/home/jing/g16/l9999.exe() [0x4ad39b]
/home/jing/g16/l9999.exe() [0x4a024f]
/home/jing/g16/l9999.exe() [0x415d18]
/home/jing/g16/l9999.exe() [0x41121b]
/home/jing/g16/l9999.exe() [0x411124]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x2b78c8950555]
/home/jing/g16/l9999.exe() [0x40b869]
Error: Optimization did not normally finish!
The optimization failed because number of allowed steps is exceeded
template3.gjf was not found in current folder! "igaucontinue=1" option is ignor
ed
Error: Opt + freq task did not normally terminated!
Wall clock time elapsed for calculating this configuration: 15961 s
*** Configuration 3 ***
Current date: 2022-03-07 Time: 21:39:42
Loading geometry 3 from the inputted trajectory file
Generating gau.gjf...
Running Gaussian: "/home/jing/g16/g16" < gau.gjf > gau.out
Error: segmentation violation
rax 0000000000000000, rbx ffffffffffffffff, rcx ffffffffffffffff
rdx 000000000001edc8, rsp 00007ffc7d264588, rbp 00007ffc7d264b00
rsi 000000000000000b, rdi 000000000001edc8, r8 0000000000000020
r9 0000000000000401, r10 00007ffc7d263960, r11 0000000000000206
r12 00007ffc7d264b48, r13 0000000000000000, r14 0000000000000000
r15 00000000000003e6
/lib64/libpthread.so.0(+0xf630) [0x2b9451433630]
/lib64/libc.so.6(kill+0x7) [0x2b9451978657]
/home/jing/g16/l502.exe() [0x475c25]
/home/jing/g16/l502.exe() [0x49b42a]
/home/jing/g16/l502.exe() [0x5183db]
/home/jing/g16/l502.exe() [0x4f72af]
/home/jing/g16/l502.exe() [0x41de12]
/home/jing/g16/l502.exe() [0x4129db]
/home/jing/g16/l502.exe() [0x4128e4]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x2b9451964555]
/home/jing/g16/l502.exe() [0x40d029]
Error: Optimization did not normally finish!
The optimization failed due to certain reason, e.g. SCF unconvergence, three atoms are lying in the same line
Generate new gau.gjf with the last unconverged geometry based on template2.gjf
Note: Unable to locate "Input orientation" field, try to load standard orientation instead
Running Gaussian: "/home/jing/g16/g16" < gau.gjf > gau.out
Error: segmentation violation
rax 0000000000000000, rbx ffffffffffffffff, rcx ffffffffffffffff
rdx 000000000001f857, rsp 00007fffa98c8a48, rbp 00007fffa98c8fc0
rsi 000000000000000b, rdi 000000000001f857, r8 0000000000000020
r9 0000000000000401, r10 00007fffa98c7e20, r11 0000000000000206
r12 00007fffa98c9008, r13 0000000000000000, r14 0000000000000000
r15 00000000000003e6
/lib64/libpthread.so.0(+0xf630) [0x2af27a827630]
/lib64/libc.so.6(kill+0x7) [0x2af27ad6c657]
/home/jing/g16/l9999.exe() [0x45da85]
/home/jing/g16/l9999.exe() [0x478bea]
/home/jing/g16/l9999.exe() [0x4ad39b]
/home/jing/g16/l9999.exe() [0x4a024f]
/home/jing/g16/l9999.exe() [0x415d18]
/home/jing/g16/l9999.exe() [0x41121b]
/home/jing/g16/l9999.exe() [0x411124]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x2af27ad58555]
/home/jing/g16/l9999.exe() [0x40b869]
Error: Optimization did not normally finish!
The optimization failed because number of allowed steps is exceeded
template3.gjf was not found in current folder! "igaucontinue=1" option is ignor
ed
Error: Opt + freq task did not normally terminated!
Wall clock time elapsed for calculating this configuration: 24980 s
*** Configuration 4 ***
Current date: 2022-03-08 Time: 04:36:02
Loading geometry 4 from the inputted trajectory file
Generating gau.gjf...
Running Gaussian: "/home/jing/g16/g16" < gau.gjf > gau.out
Fine, optimization normally converged
Note: Unable to locate "Input orientation" field, try to load standard orientation instead
Opt + freq task normally terminated
Thermal correction to Gibbs free energy: 0.633998 a.u.
Gibbs free energy: -4033.130899 a.u.
Fine, there is no imaginary frequency
Now run single point task based on the template_SP.inp in current folder
Running ORCA: "/home/jing/orca502/orca" orcaSP.inp > orcaSP.out
Deleting orcaSP.* orcaSP_*
Single point calculation normally terminated. The sum of the new single point energy and thermal correction to Gibbs free energy is -4035.179119 a.u.
Writing the converged geometry, free energy and so on to isomers.xyz
Wall clock time elapsed for calculating this configuration: 7379 s
*** Configuration 5 ***
Current date: 2022-03-08 Time: 06:39:01
Loading geometry 5 from the inputted trajectory file
Generating gau.gjf...
Running Gaussian: "/home/jing/g16/g16" < gau.gjf > gau.out
Error: segmentation violation
rax 0000000000000000, rbx ffffffffffffffff, rcx ffffffffffffffff
rdx 00000000000161e5, rsp 00007ffeae0d0338, rbp 00007ffeae0d08b0
rsi 000000000000000b, rdi 00000000000161e5, r8 0000000000000020
r9 0000000000000401, r10 00007ffeae0cf720, r11 0000000000000202
r12 00007ffeae0d08f8, r13 0000000000000000, r14 0000000000000000
r15 00000000000003e6
/lib64/libpthread.so.0(+0xf630) [0x2b942d25b630]
/lib64/libc.so.6(kill+0x7) [0x2b942d7a0657]
/home/jing/g16/l502.exe() [0x475c25]
/home/jing/g16/l502.exe() [0x49b42a]
/home/jing/g16/l502.exe() [0x5183db]
/home/jing/g16/l502.exe() [0x4f72af]
/home/jing/g16/l502.exe() [0x41de12]
/home/jing/g16/l502.exe() [0x4129db]
/home/jing/g16/l502.exe() [0x4128e4]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x2b942d78c555]
/home/jing/g16/l502.exe() [0x40d029]
Error: Optimization did not normally finish!
The optimization failed due to certain reason, e.g. SCF unconvergence, three atoms are lying in the same line
Generate new gau.gjf with the last unconverged geometry based on template2.gjf
Note: Unable to locate "Input orientation" field, try to load standard orientation instead
Running Gaussian: "/home/jing/g16/g16" < gau.gjf > gau.out
运行得出，一部分结构是可以出结果的，一部分不太行，瞎猜是template.gjf内容不太对，但作为外行，我又看不出哪里不对。
4.全部调用orca使用的文件
另一种方法，干脆全部都使用orca进行优化+频率，再使用orca计算单点，使用的traj.xyz与上一个是相同的。
以下是template.inp内容
- ! r2SCAN-3c opt freq tightSCF noautostart miniprint nopop
- %maxcore 1000
- %pal nprocs 16 end
- * xyz 0 1
- [GEOMETRY]
- *
4.全部调用orca的运行提示
*** Configuration 1 ***
Current date: 2022-03-07 Time: 14:36:04
Loading geometry 1 from the inputted trajectory file
Generating orca.inp...
Running ORCA: "/home/jing/orca502/orca" orca.inp > orca.out
Optimization converged normally
Extracting geometry from orca.xyz...
Opt + freq task normally terminated
Extracting energy from orca.out...
Thermal correction to Gibbs free energy: 0.632952 a.u.
Gibbs free energy: -4035.064697 a.u.
Fine, there is no imaginary frequency
Now run single point task based on the template_SP.inp in current folder
Running ORCA: "/home/jing/orca502/orca" orcaSP.inp > orcaSP.out
Deleting orcaSP.* orcaSP_*
Single point calculation normally terminated. The sum of the new single point energy and thermal correction to Gibbs free energy is -4035.198733 a.u.
Writing the converged geometry, free energy and so on to isomers.xyz
Wall clock time elapsed for calculating this configuration: 10913 s
*** Configuration 2 ***
Current date: 2022-03-07 Time: 17:37:57
Loading geometry 2 from the inputted trajectory file
Generating orca.inp...
Running ORCA: "/home/jing/orca502/orca" orca.inp > orca.out
Optimization converged normally
Extracting geometry from orca.xyz...
Opt + freq task normally terminated
Extracting energy from orca.out...
Thermal correction to Gibbs free energy: 0.633701 a.u.
Gibbs free energy: -4035.046441 a.u.
Fine, there is no imaginary frequency
Now run single point task based on the template_SP.inp in current folder
Running ORCA: "/home/jing/orca502/orca" orcaSP.inp > orcaSP.out
Deleting orcaSP.* orcaSP_*
Single point calculation normally terminated. The sum of the new single point energy and thermal correction to Gibbs free energy is -4035.189021 a.u.
Writing the converged geometry, free energy and so on to isomers.xyz
Wall clock time elapsed for calculating this configuration: 32190 s
全部都调用orca，就感觉要正常一些，但真的正确吗？我也不知道。
请熟悉这个方面的大佬帮忙改改作业，哪里有不对的地方，请指出。
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发表于 Post on 2022-3-4 10:31:26
楼主 Author
